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Words like cleave and egregious have meanings that are completely opposite to other meanings of the same word. How did such a bizarre, confusing state of affairs ever develop?
I mean, I just can't work out how one and the same word could come to mean two distinct things that are completely opposite! Is it the same root? What did the root mean and how did it come to be used to mean the opposite?
If you start with wikipedia
An auto-antonym (sometimes spelled autantonym), or contranym (originally spelled contronym), is a word with a homograph (a word of the same spelling) that is also an antonym (a word with the opposite meaning). Variant names include antagonym, Janus word (after the Roman god), enantiodrome, and self-antonym. It is a word with multiple meanings, one of which is defined as the reverse of one of its other meanings.
it already puts you on the right path and mentions one of the word and one of the ways that can make such words
Some pairs of contronyms are true homographs, i.e., distinct words with different etymology which happen to have the same form. For instance cleave "separate" is from Old English clēofen, while cleave "adhere" is from Old English cleofian, which was pronounced differently. This is related to false friends, but false friends do not necessarily contradict.
In other words, for example literally, the two meanings developed from the overuse of the word as hyperbole.
It's probably fair to say that the processes of language change aren't so well understood as other areas of linguistics. But, the following probably have an influence:
The evolution of language is an inherently human process. Words are coined to mean one thing, but can change based on various cultural factors, including geographic, demographic, financial, and of course historical.
For example, there is a verb used in political discussions, "to table". Common usage: "The bill to increase the police budget was tabled". What's odd is that this word means two different things depending on which side of the pond you're on: in America, the term is shorthand for "to lay on the table"; that is, to dismiss from or halt discussion. However, in Britain, the term is shorthand for "to bring to the table", that is, to introduce for discussion". Thus, "tabling" a bill is the start of the process in Britain, but a bad end in America.
This illustrates just one way the same word can evolve to have two different meanings; the shortening of phrases with opposite meanings to the same word or term. These two meanings can then coincide in the same culture if users of the two meanings become culturally commingled.
More to your case in point, let's take the word "cleave". In modern usage, the word has the connotation of a split. However, the word's original meaning is closer to "to penetrate into". Consider an axe splitting wood. The act of "cleaving" the wood happens as the axe enters into the log. If the axe continues all the way through, the log is "cleft in twain"; split in two, hence that connotation. However, if it doesn't, the log is still cleft, but as anyone who's chopped firewood before knows, an axe buried halfway into a log is difficult to remove. A similar connotation evolves from the obvious sexual underpinnings of the biblical phrase "to cleave to one another [and become one flesh]"; the "penetration" causes a bond between the two people, making them one (in many ways). So, the actual historical meaning of "cleave" thus can result in two different colloquial meanings depending on the pictured result.
As far as "egregious", I'm not sure that qualifies. The word has always (as far as Webster's concerned) been synonymous with "extraordinary". This can be good or bad depending on the subject of the adjective. The usual usage is with the connotation that what is egregious is a bad thing: "an egregious series of errors". However, the term can be used positively: "an egregious donation". The synonym to "extraordinary" is obvious if you swap one for the other, and in British English both terms are used as superlatives in both directions, good and bad. In American English, "extraordinary" is normally used to emphasize good, while "egregious" emphasizes bad.
People do sometimes use a word in a sense that could be construed as strongly (and perhaps diametrically) opposed to its usual sense (at a particular time), through simple misunderstanding of how the term is normally used. Sometime later, if that usage catches on, dictionaries that report the way people actually use the word begin including the opposed meaning as one possible legitimate definition of the word.
Thus, for example, Merriam-Webster's Collegiate Dictionary, Eleventh Edition (2003) includes this definition of infer (a word whose earliest retained definitions are "to derive as a conclusion from facts or premises" and "to guess or surmise"):
4 SUGGEST, HINT
But these words are equivalent to "express indirectly" which is the most common sense in which modern English speakers use the term imply; and imply occurs at the opposite end of a traditional imply–infer pipeline from the end at which infer occurs. According to the older understanding, a hinter implies some piece of intelligence, and a hintee infers it. According to the newish definition of infer (which goes back, in one form or another to the Seventh Collegiate of 1963, before which time Webster's labeled the "imply" meaning of the term "Erroneous"), however, inferring can take place at both ends of the pipeline.
A similar situation might have arisen in the case of inflammable, which means "capable of being easily ignited" but which early-20th-century fire marshals were concerned might be misunderstood to mean "not capable of being easily ignited"—so concerned, indeed, that they introduced flammable as a replacement word to take over the easy-ignition definition from inflammable. You might suppose that this development cleared the way for popular usage of inflammable to mean "not flammable"—the opposite of its original meaning—but Merriam-Webster's doesn't acknowledge that any such altered usage has occurred.
I don't have any sources to cite on this one, since I'm merely riding on my own observation. However, from how I understand it, this process usually takes place when one context of the word gets stuck in social memory. For example, I could say of someone, "Adam Rackis has made an egregious mistake," meaning that this is a mistake so awful that no one else would ever have made it. What sticks in people's minds, though, is the fact that I am communicating that Adam has made an horrific mistake, not the actual meaning of the word. Over time, as the connotation is remembered and the definition is not, the word "egregious" becomes associated with something terrible rather than something unusual. Thus, this kind of evolution of language is based on ignorance.
